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tetrad_cmd_algs.py
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tetrad_cmd_algs.py
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import os
from datetime import datetime
from causallearn.utils.TXT2GeneralGraph import txt2generalgraph
jar = "old/causal-cmd-1.6.1-jar-with-dependencies.jar"
stamp = str(datetime.now()).replace(" ", "_")
prefix = "old/causal_cmd_results/out_" + stamp
# Check whether the specified path exists or not
isExist = os.path.exists("old/causal_cmd_results")
if not isExist:
# Create a new directory because it does not exist
os.makedirs("causal_cmd_results")
print("A new directory, causal-cmd-results, is created.")
print("Result will be sent to this file: " + prefix + "_out.txt")
def pc(path, alpha):
os.system("java -Xmx10g -jar " + jar + " "
+ "--default "
+ "--algorithm pc "
+ "--data-type continuous "
+ "--dataset " + path + " "
+ "--test fisher-z-test "
+ "--delimiter tab "
+ "--alpha " + str(alpha) + " "
+ "--verbose "
+ "--prefix " + prefix)
return txt2generalgraph(prefix + "_out.txt")
def pcmax(path, alpha):
os.system("java -Xmx10g -jar " + jar + " "
+ "--default "
+ "--algorithm pcmax "
+ "--data-type continuous "
+ "--dataset " + path + " "
+ "--test fisher-z-test "
+ "--delimiter tab "
+ "--alpha " + str(alpha) + " "
+ "--verbose "
+ "--prefix " + prefix)
return txt2generalgraph(prefix + "_out.txt")
def fci(path, alpha):
os.system("java -Xmx10g -jar " + jar + " "
+ "--default "
+ "--algorithm fci "
+ "--data-type continuous "
+ "--dataset " + path + " "
+ "--test fisher-z-test "
+ "--delimiter tab "
+ "--alpha " + str(alpha) + " "
+ "--verbose "
+ "--prefix " + prefix)
return txt2generalgraph(prefix + "_out.txt")
def fges(path, penaltyDiscount):
os.system("java -Xmx10g -jar " + jar + " "
+ "--default "
+ "--algorithm fges "
+ "--data-type continuous "
+ "--dataset " + path + " "
+ "--score sem-bic-score "
+ "--delimiter tab "
+ "--penaltyDiscount " + str(penaltyDiscount) + " "
+ "--parallel "
+ "--verbose "
+ "--prefix " + prefix)
return txt2generalgraph(prefix + "_out.txt")
def grasp(path, penaltyDiscount):
os.system("java -Xmx10g -jar " + jar + " "
+ "--default "
+ "--algorithm grasp "
+ "--data-type continuous "
+ "--dataset " + path + " "
+ "--score sem-bic-score "
+ "--test fisher-z-test "
+ "--delimiter tab "
+ "--penaltyDiscount " + str(penaltyDiscount) + " "
+ "--verbose "
+ "--prefix " + prefix)
return txt2generalgraph(prefix + "_out.txt")
def graspfci(path, penaltyDiscount):
os.system("java -Xmx10g -jar " + jar + " "
+ "--default "
+ "--algorithm graspfci "
+ "--data-type continuous "
+ "--dataset " + path + " "
+ "--score sem-bic-score "
+ "--test fisher-z-test "
+ "--delimiter tab "
+ "--penaltyDiscount " + str(penaltyDiscount) + " "
+ "--verbose "
+ "--prefix " + prefix)
return txt2generalgraph(prefix + "_out.txt")
def boss_tuck(path, penaltyDiscount):
os.system("java -Xmx10g -jar " + jar + " "
+ "--default "
+ "--experimental "
+ "--algorithm boss-tuck "
+ "--data-type continuous "
+ "--dataset " + path + " "
+ "--score sem-bic-score "
+ "--test fisher-z-test "
+ "--delimiter tab "
+ "--graspUseScore "
+ "--penaltyDiscount " + str(penaltyDiscount) + " "
+ "--verbose "
+ "--prefix " + prefix)
return txt2generalgraph(prefix + "_out.txt")
def boss(path, penaltyDiscount):
os.system("java -Xmx10g -jar " + jar + " "
+ "--default "
+ "--experimental "
+ "--algorithm boss "
+ "--data-type continuous "
+ "--dataset " + path + " "
+ "--score sem-bic-score "
+ "--test fisher-z-test "
+ "--delimiter tab "
+ "--graspUseScore "
+ "--penaltyDiscount " + str(penaltyDiscount) + " "
+ "--verbose "
+ "--prefix " + prefix)
return txt2generalgraph(prefix + "_out.txt")
def rges(path, penaltyDiscount):
os.system("java -Xmx10g -jar " + jar + " "
+ "--default "
+ "--experimental "
+ "--algorithm rges "
+ "--data-type continuous "
+ "--dataset " + path + " "
+ "--score sem-bic-score "
+ "--delimiter tab "
+ "--penaltyDiscount " + str(penaltyDiscount) + " "
+ "--verbose "
+ "--prefix " + prefix)
return txt2generalgraph(prefix + "_out.txt")